Animate transparency of entire layer
I am not animation expert but I think what you want to do is... make your separate completed renders for organs, muscles, and then skin. then, in the compositor, create your fade-in animation from one completed render image to the next by using the alpha-over node. This example probably explains it better than I can - https://docs.blender.org/manual/en/dev/compositing/types/color/alpha_over.html